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Structure of d(TGCGCA)(2) and a comparison with other DNA Hexamers

Harper, A., Brannigan, J.A., Buck, M., Hewitt, L., Moore, M.H., Schneider, B. and Lewis, R.J. (1998) Structure of d(TGCGCA)(2) and a comparison with other DNA Hexamers. Acta Crystallographica Section D: Biological Crystallography. pp. 1273-1284. ISSN 0907-4449

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Abstract

The X-ray crystal structure of d(TGCGCA)(2) has been determined at 120 K to a resolution of 1.3 Angstrom. Hexamer duplexes, in the Z-DNA conformation, pack in an arrangement similar to the 'pure spermine form' [Egli et al. (1991). Biochemistry, 30, 11388-11402] but with significantly different cell dimensions. The phosphate backbone exists in two equally populated discrete conformations at one nucleotide step, around phosphate 11. The structure contains two ordered cobalt hexammine molecules which have roles in stabilization of both the Z-DNA conformation of the duplex and in crystal packing. A comparison of d(TGCGCA)(2) with other Z-DNA hexamer structures available in the Nucleic Acid Database illustrates the elusive nature of crystal packing. A review of the interactions with the metal cations Na+, Mg2+ and Co3+ reveals a relatively small proportion of phosphate binding and that close contacts between metal ions are common. A prediction of the water structure is compared with the observed pattern in the reported structure.

Item Type: Article
Copyright, Publisher and Additional Information: Copyright © 1998 International Union of Crystallography - http://www.iucr.org/cgi-bin/paper?jn0040
Keywords: HANDED Z-DNA, SINGLE-CRYSTAL STRUCTURE, PURE-SPERMINE FORM, MOLECULAR-STRUCTURE, BASE-PAIRS, ATOMIC RESOLUTION, AB-INITIO, FRAGMENT, BINDING, NOGALAMYCIN
Academic Units: The University of York > Chemistry (York)
Depositing User: Sherpa Assistant
Date Deposited: 11 May 2005
Last Modified: 17 Oct 2013 14:40
Published Version: http://dx.doi.org/10.1107/S0907444998002807
Status: Published
Refereed: Yes
Related URLs:
URI: http://eprints.whiterose.ac.uk/id/eprint/452

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